Variant chr1-110034695-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_033088.4(STRIP1):c.58C>T(p.Pro20Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000147 in 1,362,472 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0000015 ( 0 hom. )

Consequence

STRIP1
NM_033088.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.16

Variant links:

Genes affected

STRIP1 (HGNC:25916): (striatin interacting protein 1) This gene encodes a member of the striatin-interacting phosphatase and kinase complex, which is involved in localization of the Golgi body. The encoded protein participates in cytosketelal organization. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

STRIP1 links:

LOC105378895 (HGNC:):

LOC105378895 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.113455325).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STRIP1	NM_033088.4 linkuse as main transcript	c.58C>T	p.Pro20Ser	missense_variant	1/21	ENST00000369795.8	NP_149079.2
LOC105378895	XR_947693.3 linkuse as main transcript	n.31+714G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STRIP1	ENST00000369795.8 linkuse as main transcript	c.58C>T	p.Pro20Ser	missense_variant	1/21	1	NM_033088.4	ENSP00000358810	P1	Q5VSL9-1
STRIP1	ENST00000485775.5 linkuse as main transcript	c.58C>T	p.Pro20Ser	missense_variant, NMD_transcript_variant	1/22	1		ENSP00000476025		Q5VSL9-4
STRIP1	ENST00000369796.5 linkuse as main transcript	c.-106+3055C>T		intron_variant		2		ENSP00000358811		Q5VSL9-2
STRIP1	ENST00000489059.1 linkuse as main transcript	n.70C>T		non_coding_transcript_exon_variant	1/2	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000147

AC:

AN:

1362472

Hom.:

Cov.:

AF XY:

0.00000298

AC XY:

AN XY:

671954

show subpopulations

Gnomad4 AFR exome

AF:

0.0000364

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

9.38e-7

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Alfa

AF:

0.000112

Hom.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

May 06, 2022

The c.58C>T (p.P20S) alteration is located in exon 1 (coding exon 1) of the STRIP1 gene. This alteration results from a C to T substitution at nucleotide position 58, causing the proline (P) at amino acid position 20 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.094

BayesDel_addAF

Benign

-0.11

BayesDel_noAF

Benign

-0.39

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.022

Eigen

Benign

-0.32

Eigen_PC

Benign

-0.089

FATHMM_MKL

Benign

0.088

LIST_S2

Benign

0.82

M_CAP

Uncertain

0.099

MetaRNN

Benign

0.11

MetaSVM

Benign

-0.81

MutationAssessor

Benign

0.55

MutationTaster

Benign

0.82

D;D;D

PrimateAI

Pathogenic

0.86

PROVEAN

Benign

0.29

REVEL

Benign

0.12

Sift

Benign

0.055

Sift4G

Pathogenic

0.0

Polyphen

0.015

Vest4

0.21

MutPred

0.23

Loss of catalytic residue at P20 (P = 0.0011);

MVP

0.22

MPC

0.79

ClinPred

0.46

GERP RS

5.3

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.7

Varity_R

0.089

gMVP

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over